chisurf.common module

common.py

Common data for all scripts in the SuRF-toolbox. In the common library all kinds of constants are defined. For instance colors in plots but also constants as the Avogadros number.

chisurf.common.CHARGE_DICT = {'ARG': 1.0, 'ASP': -1.0, 'CTERM': -1.0, 'CYS': -1.0, 'GLU': -1.0, 'HIS': 1.0, 'LYS': 1.0, 'NTERM': 1.0, 'TYR': -1.0}

Default charges of amino acids

chisurf.common.MAX_BONDS = {'C': 4, 'H': 1, 'N': 4, 'O': 3, 'P': 5}

Dictionary of maximum number of bonds per atom type

chisurf.common.MW_DICT = {'ACE': 43.3, 'ALA': 89.09, 'ARG': 174.2, 'ASN': 132.12, 'ASP': 133.1, 'ASX': 132.61, 'CYS': 121.15, 'GLN': 146.15, 'GLU': 147.13, 'GLX': 146.64, 'GLY': 75.07, 'HIS': 155.16, 'ILE': 131.17, 'IVA': 85.12, 'LEU': 131.17, 'LYS': 146.19, 'MET': 149.21, 'PHE': 165.19, 'PRO': 115.13, 'SER': 105.09, 'STA': 157.15, 'THR': 119.12, 'TRP': 204.23, 'TYR': 181.19, 'VAL': 117.15}

Dictionary of amino acid molecular weights. The the molecular weight of water should be subtracted for each peptide bond to calculate a protein molecular weight.

chisurf.common.MW_H2O = 18.0

Molecular weight of water

chisurf.common.PKA_DICT = {'ARG': 12.0, 'ASP': 4.0, 'CTERM': 3.1, 'CYS': 8.5, 'GLU': 4.4, 'HIS': 6.5, 'LYS': 10.4, 'NTERM': 8.0, 'TYR': 10.0}

Dictionary of pKa values and un-protonated charge state.

chisurf.common.TITR_ATOM = {'ARG': 'CZ ', 'ASP': 'CG ', 'GLU': 'CD ', 'HIS': 'NE2', 'LYS': 'NZ ', 'TYR': 'OH '}

Atom on which to place charge in amino-acid

chisurf.common.TITR_ATOM_COARSE = {'ARG': 'CB', 'ASP': 'CB', 'CYS': 'CB', 'GLU': 'CB', 'HIS': 'CB', 'LYS': 'CB', 'TYR': 'CB'}

Atom on which to place charge in amino-acid (Coarse grained default position C-Beta)

chisurf.common.VDW_DICT = {'Ac': 2.0, 'Ag': 1.72, 'Al': 2.0, 'Am': 2.0, 'Ar': 1.88, 'As': 1.85, 'At': 2.0, 'Au': 1.66, 'B': 2.0, 'Ba': 2.0, 'Be': 2.0, 'Bh': 2.0, 'Bi': 2.0, 'Bk': 2.0, 'Br': 1.85, 'C': 1.7, 'Ca': 2.0, 'Cd': 1.58, 'Ce': 2.0, 'Cf': 2.0, 'Cl': 1.75, 'Cm': 2.0, 'Co': 2.0, 'Cr': 2.0, 'Cs': 2.0, 'Cu': 1.4, 'Db': 2.0, 'Ds': 2.0, 'Dy': 2.0, 'Er': 2.0, 'Es': 2.0, 'Eu': 2.0, 'F': 1.47, 'Fe': 2.0, 'Fm': 2.0, 'Fr': 2.0, 'Ga': 1.87, 'Gd': 2.0, 'Ge': 2.0, 'H': 1.09, 'He': 1.4, 'Hf': 2.0, 'Hg': 1.55, 'Ho': 2.0, 'Hs': 2.0, 'I': 1.98, 'In': 1.93, 'Ir': 2.0, 'K': 2.75, 'Kr': 2.02, 'La': 2.0, 'Li': 1.82, 'Lr': 2.0, 'Lu': 2.0, 'Md': 2.0, 'Mg': 1.73, 'Mn': 2.0, 'Mo': 2.0, 'Mt': 2.0, 'N': 1.55, 'Na': 2.27, 'Nb': 2.0, 'Nd': 2.0, 'Ne': 1.54, 'Ni': 1.63, 'No': 2.0, 'Np': 2.0, 'O': 1.52, 'Os': 2.0, 'P': 1.8, 'Pa': 2.0, 'Pb': 2.02, 'Pd': 1.63, 'Pm': 2.0, 'Po': 2.0, 'Pr': 2.0, 'Pt': 1.72, 'Pu': 2.0, 'Ra': 2.0, 'Rb': 2.0, 'Re': 2.0, 'Rf': 2.0, 'Rh': 2.0, 'Rn': 2.0, 'Ru': 2.0, 'S': 1.8, 'Sb': 2.0, 'Sc': 2.0, 'Se': 1.9, 'Sg': 2.0, 'Si': 2.1, 'Sm': 2.0, 'Sn': 2.17, 'Sr': 2.0, 'Ta': 2.0, 'Tb': 2.0, 'Tc': 2.0, 'Te': 2.06, 'Th': 2.0, 'Ti': 2.0, 'Tl': 1.96, 'Tm': 2.0, 'U': 1.86, 'V': 2.0, 'W': 2.0, 'Xe': 2.16, 'Y': 2.0, 'Yb': 2.0, 'Zn': 1.39, 'Zr': 2.0}

Dictionary of van der Waal radii CR - coarse grained Carbon/Calpha

chisurf.common.atom_weights = {'Ac': 227.0, 'Ag': 107.868, 'Al': 26.982, 'Am': 243.0, 'Ar': 39.948, 'As': 74.922, 'At': 210.0, 'Au': 196.967, 'B': 10.811, 'Ba': 137.327, 'Be': 9.012, 'Bh': 264.0, 'Bi': 208.98, 'Bk': 247.0, 'Br': 79.904, 'C': 12.011, 'Ca': 40.078, 'Cd': 112.411, 'Ce': 140.116, 'Cf': 251.0, 'Cl': 35.453, 'Cm': 247.0, 'Co': 58.933, 'Cr': 51.996, 'Cs': 132.905, 'Cu': 63.546, 'Db': 262.0, 'Ds': 271.0, 'Dy': 162.5, 'Er': 167.26, 'Es': 252.0, 'Eu': 151.964, 'F': 18.998, 'Fe': 55.845, 'Fm': 257.0, 'Fr': 223.0, 'Ga': 69.723, 'Gd': 157.25, 'Ge': 72.61, 'H': 1.008, 'He': 4.003, 'Hf': 178.49, 'Hg': 200.59, 'Ho': 164.93, 'Hs': 269.0, 'I': 126.904, 'In': 114.818, 'Ir': 192.217, 'K': 39.098, 'Kr': 83.8, 'La': 138.906, 'Li': 6.941, 'Lr': 262.0, 'Lu': 174.967, 'Md': 258.0, 'Mg': 24.305, 'Mn': 54.938, 'Mo': 95.94, 'Mt': 268.0, 'N': 14.007, 'Na': 22.991, 'Nb': 92.906, 'Nd': 144.24, 'Ne': 20.18, 'Ni': 58.693, 'No': 259.0, 'Np': 237.0, 'O': 15.999, 'Os': 190.23, 'P': 30.974, 'Pa': 231.036, 'Pb': 207.2, 'Pd': 106.42, 'Pm': 145.0, 'Po': 210.0, 'Pr': 140.908, 'Pt': 195.078, 'Pu': 244.0, 'Ra': 226.0, 'Rb': 85.468, 'Re': 186.207, 'Rf': 261.0, 'Rh': 102.906, 'Rn': 222.0, 'Ru': 101.07, 'S': 32.066, 'Sb': 121.76, 'Sc': 44.956, 'Se': 78.96, 'Sg': 266.0, 'Si': 28.086, 'Sm': 150.36, 'Sn': 118.71, 'Sr': 87.62, 'Ta': 180.948, 'Tb': 158.925, 'Tc': 98.0, 'Te': 127.6, 'Th': 232.038, 'Ti': 47.867, 'Tl': 204.383, 'Tm': 168.934, 'U': 238.029, 'V': 50.942, 'W': 183.84, 'Xe': 131.29, 'Y': 88.906, 'Yb': 173.04, 'Zn': 65.39, 'Zr': 91.224}

//www.chem.qmul.ac.uk/iupac/AtWt/ & PyMol)

Type

Atomic weights (http

chisurf.common.quencher_names = dict_keys(['TRP', 'MET', 'TYR', 'HIS', 'PRO'])

Definition of quenching amino-acids and quenching atoms of quencher